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Rhodium in PDB 7qpz: X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4):
4.6.1.18;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4), PDB code: 7qpz was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.86 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.73, 32.87, 72.89, 90, 90.15, 90
R / Rfree (%) 16.2 / 20.2

Other elements in 7qpz:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Rhodium Binding Sites:

The binding sites of Rhodium atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) (pdb code 7qpz). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 8 binding sites of Rhodium where determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4), PDB code: 7qpz:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Rhodium binding site 1 out of 8 in 7qpz

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Rhodium binding site 1 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:16.8
occ:0.75
 RH1 A:F5T201 0.0 16.8 0.8
O1 A:F5T201 2.1 16.6 0.8
O7 A:F5T201 2.1 17.0 0.8
O3 A:F5T201 2.1 19.6 0.8
O A:HOH356 2.1 18.7 0.8
O0 A:F5T201 2.1 18.9 0.8
RH2 A:F5T201 2.4 11.8 0.8
C5 A:F5T201 2.9 24.6 0.8
C3 A:F5T201 2.9 15.9 0.8
C1 A:F5T201 3.0 14.0 0.8
O2 A:F5T201 3.1 14.0 0.8
O8 A:F5T201 3.1 14.8 0.8
O4 A:F5T201 3.2 16.2 0.8
O9 A:F5T201 3.2 15.6 0.8
HZ3 A:LYS7 3.7 27.9 1.0
HD1 A:HIS119 3.8 10.5 0.0
O A:HOH418 4.1 24.9 1.0
HE2 A:LYS7 4.2 24.5 1.0
HZ2 A:LYS7 4.3 27.9 1.0
C6 A:F5T201 4.3 33.2 0.8
NZ A:LYS7 4.4 29.5 1.0
C4 A:F5T201 4.4 16.5 0.8
C2 A:F5T201 4.4 13.9 0.8
O A:HOH367 4.5 13.8 0.3
ND1 A:HIS119 4.6 10.5 1.0
O A:HOH310 4.7 30.8 1.0
O A:HOH465 4.7 29.8 1.0
CE A:LYS7 4.8 24.7 1.0
HD3 A:LYS7 4.8 20.0 1.0
HB2 A:HIS119 4.8 9.5 1.0
F1 A:F5T201 4.8 33.5 0.8
F3 A:F5T201 4.8 41.5 0.8

Rhodium binding site 2 out of 8 in 7qpz

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Rhodium binding site 2 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh201

b:11.8
occ:0.75
 RH2 A:F5T201 0.0 11.8 0.8
HD1 A:HIS119 1.4 10.5 0.0
O2 A:F5T201 2.1 14.0 0.8
O4 A:F5T201 2.1 16.2 0.8
O8 A:F5T201 2.1 14.8 0.8
O9 A:F5T201 2.1 15.6 0.8
ND1 A:HIS119 2.3 10.5 1.0
RH1 A:F5T201 2.4 16.8 0.8
C5 A:F5T201 2.9 24.6 0.8
C3 A:F5T201 2.9 15.9 0.8
C1 A:F5T201 3.0 14.0 0.8
HB2 A:HIS119 3.0 9.5 1.0
O0 A:F5T201 3.1 18.9 0.8
O1 A:F5T201 3.1 16.6 0.8
O7 A:F5T201 3.1 17.0 0.8
O3 A:F5T201 3.2 19.6 0.8
CE1 A:HIS119 3.2 12.9 1.0
HE1 A:HIS119 3.3 11.9 1.0
CG A:HIS119 3.3 10.1 1.0
CB A:HIS119 3.6 9.5 1.0
O A:HOH329 3.9 12.2 1.0
HA A:HIS119 3.9 8.7 1.0
O A:HOH395 4.1 20.4 1.0
NE2 A:HIS119 4.3 11.5 1.0
C6 A:F5T201 4.3 33.2 0.8
C4 A:F5T201 4.4 16.5 0.8
CA A:HIS119 4.4 8.8 1.0
C2 A:F5T201 4.4 13.9 0.8
CD2 A:HIS119 4.4 11.6 1.0
HB3 A:HIS119 4.4 9.4 1.0
O A:HOH356 4.4 18.7 0.8
O A:HOH310 4.5 30.8 1.0
O A:VAL118 4.6 10.2 1.0
O A:HOH389 4.7 23.0 1.0
F2 A:F5T201 4.7 43.6 0.8
O A:HOH472 4.8 37.7 1.0
O A:HOH402 4.8 36.4 1.0
O A:HOH303 4.8 38.7 1.0
F3 A:F5T201 4.9 41.5 0.8
H A:PHE120 4.9 7.9 1.0

Rhodium binding site 3 out of 8 in 7qpz

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Rhodium binding site 3 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:21.3
occ:0.55
 RH1 A:F5I202 0.0 21.3 0.6
O6 A:F5I202 2.1 22.6 0.6
O7 A:F5I202 2.1 19.8 0.6
O1 A:F5I202 2.1 18.9 0.6
O3 A:F5I202 2.1 20.1 0.6
O A:HOH449 2.3 22.4 0.6
RH2 A:F5I202 2.4 13.5 0.6
C1 A:F5I202 2.9 20.1 0.6
C3 A:F5I202 2.9 19.9 0.6
O8 A:F5I202 3.0 16.9 0.6
O2 A:F5I202 3.1 15.1 0.6
O5 A:F5I202 3.1 18.2 0.6
O4 A:F5I202 3.2 19.1 0.6
HE2 A:HIS105 3.7 12.5 0.0
C4 A:F5I202 4.4 19.3 0.6
C2 A:F5I202 4.4 17.7 0.6
O A:HOH314 4.6 43.1 1.0
NE2 A:HIS105 4.6 12.5 1.0
O A:HOH451 4.6 43.2 1.0
O A:HOH505 4.9 28.4 1.0

Rhodium binding site 4 out of 8 in 7qpz

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Rhodium binding site 4 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rh202

b:13.5
occ:0.55
 RH2 A:F5I202 0.0 13.5 0.6
HE2 A:HIS105 1.3 12.5 0.0
O5 A:F5I202 2.1 18.2 0.6
O2 A:F5I202 2.1 15.1 0.6
O4 A:F5I202 2.1 19.1 0.6
O8 A:F5I202 2.1 16.9 0.6
NE2 A:HIS105 2.2 12.5 1.0
RH1 A:F5I202 2.4 21.3 0.6
C1 A:F5I202 2.9 20.1 0.6
C3 A:F5I202 3.0 19.9 0.6
O3 A:F5I202 3.1 20.1 0.6
O1 A:F5I202 3.1 18.9 0.6
CE1 A:HIS105 3.1 12.9 1.0
O7 A:F5I202 3.2 19.8 0.6
O6 A:F5I202 3.2 22.6 0.6
CD2 A:HIS105 3.2 12.6 1.0
HE1 A:HIS105 3.3 12.7 1.0
HD2 A:HIS105 3.4 12.1 1.0
O A:HOH316 4.0 33.0 1.0
O A:HOH434 4.2 43.5 1.0
HG21 A:THR78 4.3 14.0 1.0
ND1 A:HIS105 4.3 12.3 1.0
O A:HOH360 4.3 22.6 1.0
CG A:HIS105 4.3 10.6 1.0
HG23 A:THR78 4.3 14.0 1.0
C2 A:F5I202 4.4 17.7 0.6
C4 A:F5I202 4.5 19.3 0.6
O A:HOH314 4.5 43.1 1.0
CG2 A:THR78 4.7 14.3 1.0
HG22 A:THR78 4.7 14.0 1.0
O A:HOH449 4.8 22.4 0.6

Rhodium binding site 5 out of 8 in 7qpz

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Rhodium binding site 5 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 5 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:13.0
occ:0.30
 RH1 B:F5I201 0.0 13.0 0.3
RH1 B:F5I201 0.6 13.7 0.3
HD1 B:HIS119 1.5 15.9 0.0
O3 B:F5I201 1.6 18.8 0.3
O6 B:F5I201 1.9 14.5 0.3
O1 B:F5I201 2.1 13.9 0.3
O3 B:F5I201 2.1 14.4 0.3
O7 B:F5I201 2.1 14.3 0.3
O6 B:F5I201 2.1 15.5 0.3
ND1 B:HIS119 2.3 15.9 1.0
RH2 B:F5I201 2.4 18.5 0.3
RH2 B:F5I201 2.4 16.7 0.3
O7 B:F5I201 2.4 15.9 0.3
O1 B:F5I201 2.6 16.1 0.3
O4 B:F5I201 2.8 19.4 0.3
C1 B:F5I201 2.9 13.3 0.3
O2 B:F5I201 2.9 14.2 0.3
O5 B:F5I201 3.0 18.5 0.3
CE1 B:HIS119 3.1 18.6 1.0
O5 B:F5I201 3.1 17.8 0.3
HE1 B:HIS119 3.1 17.8 1.0
O2 B:F5I201 3.1 17.1 0.3
C3 B:F5I201 3.1 14.8 0.3
O8 B:F5I201 3.1 16.8 0.3
C3 B:F5I201 3.2 16.2 0.3
C1 B:F5I201 3.2 15.9 0.3
O4 B:F5I201 3.3 16.0 0.3
HB2 B:HIS119 3.3 11.6 1.0
CG B:HIS119 3.4 15.2 1.0
O8 B:F5I201 3.4 15.1 0.3
O B:HOH306 3.7 15.7 1.0
HA B:HIS119 3.7 9.5 1.0
CB B:HIS119 3.8 11.2 1.0
O B:HOH441 4.2 28.6 1.0
NE2 B:HIS119 4.3 18.5 1.0
CA B:HIS119 4.3 9.6 1.0
C2 B:F5I201 4.3 12.6 0.3
CD2 B:HIS119 4.4 16.0 1.0
C4 B:F5I201 4.5 14.0 0.3
O B:VAL118 4.6 11.1 1.0
O B:HOH402 4.6 34.0 1.0
H B:PHE120 4.6 9.1 1.0
C4 B:F5I201 4.6 17.0 0.3
HB3 B:HIS119 4.7 11.6 1.0
C2 B:F5I201 4.7 15.3 0.3
O B:HOH386 4.7 21.5 0.6
O B:HOH334 4.7 10.9 0.4
O B:HOH409 4.8 34.7 1.0
O B:HOH371 4.8 19.3 1.0
O B:HOH304 4.9 37.3 1.0

Rhodium binding site 6 out of 8 in 7qpz

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Rhodium binding site 6 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 6 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:13.7
occ:0.30
 RH1 B:F5I201 0.0 13.7 0.3
RH1 B:F5I201 0.6 13.0 0.3
HD1 B:HIS119 1.4 15.9 0.0
O7 B:F5I201 1.7 14.3 0.3
O3 B:F5I201 1.8 14.4 0.3
O1 B:F5I201 2.1 16.1 0.3
O6 B:F5I201 2.1 14.5 0.3
O7 B:F5I201 2.1 15.9 0.3
O3 B:F5I201 2.1 18.8 0.3
ND1 B:HIS119 2.3 15.9 1.0
RH2 B:F5I201 2.4 16.7 0.3
O1 B:F5I201 2.4 13.9 0.3
RH2 B:F5I201 2.5 18.5 0.3
O6 B:F5I201 2.6 15.5 0.3
C3 B:F5I201 2.7 14.8 0.3
C1 B:F5I201 2.8 15.9 0.3
O2 B:F5I201 2.8 17.1 0.3
C3 B:F5I201 2.9 16.2 0.3
O8 B:F5I201 3.0 16.8 0.3
HB2 B:HIS119 3.0 11.6 1.0
O4 B:F5I201 3.0 16.0 0.3
CE1 B:HIS119 3.1 18.6 1.0
O2 B:F5I201 3.1 14.2 0.3
O8 B:F5I201 3.1 15.1 0.3
C1 B:F5I201 3.2 13.3 0.3
HE1 B:HIS119 3.2 17.8 1.0
CG B:HIS119 3.3 15.2 1.0
O4 B:F5I201 3.3 19.4 0.3
O5 B:F5I201 3.3 18.5 0.3
O5 B:F5I201 3.4 17.8 0.3
CB B:HIS119 3.6 11.2 1.0
O B:HOH441 3.7 28.6 1.0
HA B:HIS119 3.8 9.5 1.0
C4 B:F5I201 4.1 14.0 0.3
O B:HOH306 4.1 15.7 1.0
CA B:HIS119 4.2 9.6 1.0
NE2 B:HIS119 4.2 18.5 1.0
C2 B:F5I201 4.3 15.3 0.3
CD2 B:HIS119 4.3 16.0 1.0
C4 B:F5I201 4.4 17.0 0.3
HB3 B:HIS119 4.4 11.6 1.0
O B:VAL118 4.4 11.1 1.0
O B:HOH409 4.5 34.7 1.0
C2 B:F5I201 4.6 12.6 0.3
O B:HOH386 4.7 21.5 0.6
H B:PHE120 4.9 9.1 1.0

Rhodium binding site 7 out of 8 in 7qpz

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Rhodium binding site 7 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 7 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:16.7
occ:0.30
 RH2 B:F5I201 0.0 16.7 0.3
RH2 B:F5I201 0.6 18.5 0.3
O2 B:F5I201 1.7 17.1 0.3
O8 B:F5I201 1.8 16.8 0.3
O8 B:F5I201 2.1 15.1 0.3
O5 B:F5I201 2.1 18.5 0.3
O4 B:F5I201 2.1 16.0 0.3
O2 B:F5I201 2.1 14.2 0.3
RH1 B:F5I201 2.4 13.7 0.3
RH1 B:F5I201 2.4 13.0 0.3
O B:HOH386 2.4 21.5 0.6
O5 B:F5I201 2.5 17.8 0.3
O4 B:F5I201 2.6 19.4 0.3
C1 B:F5I201 2.6 15.9 0.3
C3 B:F5I201 2.6 16.2 0.3
O7 B:F5I201 2.7 14.3 0.3
C3 B:F5I201 2.7 14.8 0.3
O7 B:F5I201 2.9 15.9 0.3
O3 B:F5I201 3.0 14.4 0.3
O1 B:F5I201 3.0 16.1 0.3
O3 B:F5I201 3.0 18.8 0.3
C1 B:F5I201 3.0 13.3 0.3
O1 B:F5I201 3.3 13.9 0.3
O6 B:F5I201 3.3 14.5 0.3
O6 B:F5I201 3.4 15.5 0.3
O B:HOH400 3.7 44.0 1.0
HZ3 B:LYS7 3.8 23.6 1.0
HD1 B:HIS119 3.8 15.9 0.0
O B:HOH448 4.0 36.9 1.0
C2 B:F5I201 4.0 15.3 0.3
C4 B:F5I201 4.1 17.0 0.3
HZ2 B:LYS7 4.2 23.6 1.0
C4 B:F5I201 4.2 14.0 0.3
HE2 B:LYS7 4.2 20.3 1.0
O B:HOH481 4.3 40.6 1.0
HD3 B:LYS7 4.3 16.4 1.0
NZ B:LYS7 4.3 25.5 1.0
C2 B:F5I201 4.5 12.6 0.3
ND1 B:HIS119 4.6 15.9 1.0
O B:HOH321 4.6 21.4 1.0
CE B:LYS7 4.7 19.9 1.0
HB2 B:HIS119 4.8 11.6 1.0

Rhodium binding site 8 out of 8 in 7qpz

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Rhodium binding site 8 out of 8 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 8 of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Rh201

b:18.5
occ:0.30
 RH2 B:F5I201 0.0 18.5 0.3
RH2 B:F5I201 0.6 16.7 0.3
O5 B:F5I201 1.7 18.5 0.3
O2 B:F5I201 1.8 14.2 0.3
O5 B:F5I201 2.1 17.8 0.3
O2 B:F5I201 2.1 17.1 0.3
O8 B:F5I201 2.1 16.8 0.3
O4 B:F5I201 2.1 19.4 0.3
RH1 B:F5I201 2.4 13.0 0.3
O B:HOH386 2.4 21.5 0.6
RH1 B:F5I201 2.5 13.7 0.3
O4 B:F5I201 2.6 16.0 0.3
O8 B:F5I201 2.6 15.1 0.3
C1 B:F5I201 2.7 13.3 0.3
O3 B:F5I201 2.8 18.8 0.3
O1 B:F5I201 3.0 13.9 0.3
O7 B:F5I201 3.0 14.3 0.3
C3 B:F5I201 3.0 16.2 0.3
O6 B:F5I201 3.1 15.5 0.3
C1 B:F5I201 3.1 15.9 0.3
O6 B:F5I201 3.2 14.5 0.3
C3 B:F5I201 3.2 14.8 0.3
O7 B:F5I201 3.2 15.9 0.3
O3 B:F5I201 3.2 14.4 0.3
O1 B:F5I201 3.4 16.1 0.3
HZ3 B:LYS7 3.4 23.6 1.0
HE2 B:LYS7 3.7 20.3 1.0
HZ2 B:LYS7 3.7 23.6 1.0
HD1 B:HIS119 3.8 15.9 0.0
NZ B:LYS7 3.9 25.5 1.0
HD3 B:LYS7 4.0 16.4 1.0
O B:HOH448 4.1 36.9 1.0
C2 B:F5I201 4.1 12.6 0.3
CE B:LYS7 4.2 19.9 1.0
O B:HOH400 4.2 44.0 1.0
C4 B:F5I201 4.5 17.0 0.3
C2 B:F5I201 4.5 15.3 0.3
O B:HOH481 4.5 40.6 1.0
O B:HOH321 4.6 21.4 1.0
ND1 B:HIS119 4.6 15.9 1.0
CD B:LYS7 4.7 16.8 1.0
C4 B:F5I201 4.7 14.0 0.3
HE21 B:GLN11 4.7 19.7 1.0
HZ1 B:LYS7 4.8 23.6 1.0
O B:HOH371 4.8 19.3 1.0
O B:HOH334 4.9 10.9 0.4

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins. Dalton Trans V. 51 3695 2022.
ISSN: ESSN 1477-9234
PubMed: 35166290
DOI: 10.1039/D2DT00082B
Page generated: Thu Oct 10 12:37:37 2024

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